Placeholder image of a protein
Icon representing a puzzle

1894: Symmetric Trimer Design: H-bond Networks

Closed since over 5 years ago

Intermediate Overall Design Symmetry

Summary

Created
September 24, 2020
Expires
Max points
100
Description

Design a symmetric protein trimer, with 3 identical chains that assemble together! Note the Interaction Energy Objective, which will penalize poorly-scoring large residues that can lead to unwanted protein aggregation. The H-bond Network Objective encourages players to build buried, satisfied H-bond networks at the interface between symmetric chains. H-bond networks are a great way to introduce polar residues at the interface, but it's important that all of the bondable atoms make hydrogen bonds! We've also adjusted the H-bond Network Objective so that poor-scoring H-bonds may not contribute to networks; poor-scoring H-bonds will be displayed in red. This puzzle uses the Buried Unsats Objective, with a large penalty for buried polar atoms that can't make H-bonds. In this puzzle, there are no limits on the Complex Core, but we've included the Complex Core objective so players can see the core residues that can be incorporated into H-bond Networks.

Top groups

  1. Avatar for SETI.Germany 11. SETI.Germany 2 pts. 16,692
  2. Avatar for BOINC@Poland 12. BOINC@Poland 1 pt. 16,195
  3. Avatar for Team Canada 13. Team Canada 1 pt. 10,638
  4. Avatar for IB BIO 1 14. IB BIO 1 1 pt. 0
  5. Avatar for Montessori High School 15. Montessori High School 1 pt. 0
  6. Avatar for Foldit Staff 16. Foldit Staff 1 pt. 0
  7. Avatar for CH362_ButlerUniversity 17. CH362_ButlerUniversity 1 pt. 0
  8. Avatar for DSN @ Home 18. DSN @ Home 1 pt. 0
  1. Avatar for Czim 51. Czim Lv 1 6 pts. 17,662
  2. Avatar for Hellcat6 52. Hellcat6 Lv 1 6 pts. 17,469
  3. Avatar for CAN1958 53. CAN1958 Lv 1 5 pts. 17,399
  4. Avatar for alcor29 54. alcor29 Lv 1 5 pts. 17,319
  5. Avatar for momadoc 55. momadoc Lv 1 5 pts. 17,307
  6. Avatar for fishercat 56. fishercat Lv 1 4 pts. 17,170
  7. Avatar for kyoota 57. kyoota Lv 1 4 pts. 17,084
  8. Avatar for Dhalion 58. Dhalion Lv 1 4 pts. 16,861
  9. Avatar for HMK 59. HMK Lv 1 3 pts. 16,692
  10. Avatar for fpc 60. fpc Lv 1 3 pts. 16,561

Comments

bkoep Staff Lv 1

It's hard to make blanket conclusions about all H-bond networks. But we have definitely noticed a general improvement in the quality of H-bond networks since those changes – especially in the top-ranking solutions.

Before, it was not unusual for us to find a few "unrealistic" H-bond networks (usually with subtle problems in H-bond geometry) among the top-scoring solutions from a puzzle. It seemed these networks were being awarded a big bonus that did not represent a true improvement in design quality.

It makes sense that it's harder to create networks with the recent changes. But it appears that the new HBNet Objective is in fact better about awarding bonuses that reflect real improvements in solutions. (At least, the solutions look better to Foldit scientists; we won't really know about any improvements until we get to test the designs in the lab).

Formula350 Lv 1

So I won't ping you over Discord :P
However, we're all getting an error, even with the latest update:

downloading: http://fold.it/portal/files/puzzle_pdb/puzzle_post_2053.zip has key .ocmdline has key .sym has key .roscript TASKOPERATIONS SCOREFXNS FILTERS MOVERS APPLY_TO_POSE PROTOCOLS has key .owts Exception: Both weights file and score function name supplied. in ..\..\..\source\src\standalone\application\boinc\Puzzle.cc line 1403

bkoep Staff Lv 1

Thanks! Should be fixed.

Also, the September 23 update is required to open this puzzle.

spvincent Lv 1

Since the changes to H-Bond Network scoring a few puzzles ago, which were largely aimed at preventing serine triangles and similar constructs, I've found it a lot harder to create networks of any kind. If this means that the new version reflects reality better than so be it, but I can't help wondering if the changes may have been too restrictive.

bkoep Staff Lv 1

It's hard to make blanket conclusions about all H-bond networks. But we have definitely noticed a general improvement in the quality of H-bond networks since those changes – especially in the top-ranking solutions.

Before, it was not unusual for us to find a few "unrealistic" H-bond networks (usually with subtle problems in H-bond geometry) among the top-scoring solutions from a puzzle. It seemed these networks were being awarded a big bonus that did not represent a true improvement in design quality.

It makes sense that it's harder to create networks with the recent changes. But it appears that the new HBNet Objective is in fact better about awarding bonuses that reflect real improvements in solutions. (At least, the solutions look better to Foldit scientists; we won't really know about any improvements until we get to test the designs in the lab).